Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Synpcc7942_2495 Synpcc7942_2495 integral membrane protein of the ABC-type Nat permease for neutral amino acids NatD
Query= TCDB::P74318 (286 letters) >FitnessBrowser__SynE:Synpcc7942_2495 Length = 313 Score = 141 bits (355), Expect = 2e-38 Identities = 99/306 (32%), Positives = 166/306 (54%), Gaps = 25/306 (8%) Query: 1 MDLSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTW---------- 50 MD Q + NG+A+G + AL A+G TL + IL + NFAHG TL AYLT+ Sbjct: 1 MDWLQPLINGLAIGGVYALFALGYTLVFSILGVINFAHGAVFTLGAYLTYALVGGRFSFN 60 Query: 51 --WANTS---GINLWLSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALF 105 AN + + L++ LG + A + E + ++P+R R+A +I S+G+A+F Sbjct: 61 GLLANAALPFSLPFALALLLGSLLAGGASLLIEQVAFRPLRRRQADPLLTLISSLGVAVF 120 Query: 106 LRNGILLIWGGNNQNYRVPI---VPAQDFMG-----IKFEYYRLLVIAMAIAAMVVLHLI 157 + N I ++ G + I +P+ +G I+ ++++ +AIA +L + Sbjct: 121 IVNLIQILVGAEIYTFPSNIYGDLPSAINLGSSDRPIQIRTVQIILFVVAIAMFSLLTWL 180 Query: 158 LQRTKVGKAMRAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLK-PNM 216 + T+VG A++AVA++ A + GI+ + + T+ ++ VL L G++ G ++ P Sbjct: 181 INGTRVGHALKAVAEDATTASLLGIDPDRYIRLTFFLSGVLGGLAGTLVGTSVSITGPYF 240 Query: 217 GWFLILPMFASVILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFI 276 G L + ++LGG+GN G IAGG+++G+A E VP + Y+ VA L+ +L I Sbjct: 241 GIAYGLKGLSVMVLGGLGNIPGTIAGGLLLGLA-EAWVPPQWSGYRDAVAFALLFAMLLI 299 Query: 277 RPQGLF 282 RPQGLF Sbjct: 300 RPQGLF 305 Lambda K H 0.329 0.143 0.450 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 237 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 286 Length of database: 313 Length adjustment: 27 Effective length of query: 259 Effective length of database: 286 Effective search space: 74074 Effective search space used: 74074 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory